I upgraded 8 to 9.1 and it crashed during installation. As this is a private server I just stopped working on it as I had other things to do. About a week ago I set to fix it. Got it up and running for one login and then ran into a 9.1 error and couldn't log on anymore.
Got that fixed and found most of my apps are missing, looked to reinstall them and they are not listed in the apps installer..
All I want is what to do to fix it so I can continue to use OwnCloud
In order to help you out here we need to know which apps got disabled/removed.
Usually this is because the apps are not available for the upgraded server version.
Sorry, but I guess I am pretty upset about the whole upgrade process.
The ones I care about are calendar, contacts and email. The ones I have are files and gallery.
Keep in mind that I at the beginning, the crashed upgrade from 8.x to 9.x, I couldn't get into OwnCloud at all. I fixed it by deleting all the data in the links field in the database. At that point I could get into OwnCloud but some of the apps were missing.
Thanks for your help, Jim
Then try to install the apps now. Hopefully this is helping - TBH there is not really much info in your reports to give better help. 
The applications are not in the list. There was a comment on your board that the problem is the default App Store is messed up and to point the App Store to a location that had "marketplace" in the url.
That had an effect, more apps. But "Contacts won't install and "Calendar" isn't available in that store.
So I have to make a decision seeing as how 9 seems to me to be broken.
https://owncloud.org/blog/good-bye-apps-owncloud-com/
Contacts: https://marketplace.owncloud.com/apps/contacts
Calendar: https://marketplace.owncloud.com/apps/calendar
You can close this thread.
Didn't solve the problem but back leveled to 8.x